Hi Daniel,
eddy and eddy_correct are two very different things. eddy_correct is the
linear registration-based correction for eddy currents and head motion
that has been around in FSL a long time. eddy is Jesper's brand new beta
tool for correcting much larger and nonlinear eddy currents that we have
on our Human Connectome Project scanner because of its special stronger
gradients. It takes MUCH longer to run and requires specialized data,
whereas eddy_correct will run faster on any kind of diffusion data.
Peace,
Matt.
On 10/23/12 2:28 PM, "Drane, Daniel L" <[log in to unmask]> wrote:
>To add to this question, our neurosurgeon gave me a DTI scan for which he
>wants me to use probtrac to find the arcuate fasciculus. I started to run
>eddy-correct on this but discovered it does not appear to be an option
>with the new fsl version. This data was not acquired with phase
>reversals. Can I use "eddy" on this or do I have to do something else?
>
>Thanks
>
>
>Daniel L. Drane, Ph.D., ABPP(CN)
>Assistant Professor of Neurology
>Emory University School of Medicine
>Woodruff Memorial Research Building
>101 Woodruff Circle, Suite 6111
>Mailstop 1930-001-1AN
>Atlanta, Georgia 30322
>(404)727-2844 (office phone)
>[log in to unmask]
>
>Affiliate Associate Professor of Neurology
>University of Washington School of Medicine
>[log in to unmask]
>
>
>
>
>
>On 10/23/12 3:22 PM, "Marenco, Stefano (NIH/NIMH) [E]"
><[log in to unmask]> wrote:
>
>>Hi Jesper,
>>we are running some sample data through the FSL pipeline for distortion
>>correction and have a few questions.
>>We ran top-up on our b=0 images and wanted to feed the results to eddy,
>>but we don't have a guide on the FSL website yet. Could you please send
>>an example of the command line? I assume something like:
>>eddy --imain=DWIseries --mask=brain_mask --acqp=acqparams.txt
>>--index=index.txt --bvecs=bvecs --bvals=bvals --topup=topup_output
>>--out=eddy_out
>>
>>We have also acquired phase-up and down for all the diffusion volumes we
>>have. What is your experience on this point? Is it better to run top-up
>>on each individual image or to just apply the b=0 warp? Any detail on
>>this issue would be useful.
>>
>>Finally, does eddy rotate the b-matrix according to the movement of the
>>head?
>>
>>Stefano Marenco, MD
>>NIMH/CBDB
>>10 Center Drive, Bldg 10 room 3C103
>>Bethesda MD 20892
>>Tel 301 435-8964
>>Fax 301 480-7795
>>Email: [log in to unmask]
>
>
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